The Epidemiology Branch is conducting a number of birth defect studies in collaboration with the Health Research Board and Trinity College, Dublin, Ireland. The main objective of these studies is to determine the relationship between folate and birth defects. The birth defects studied to date are neural tube defects (NTDs), oral clefts, congenital heart defects, Down syndrome and omphalocele. These studies focus on biochemical factors in the area of folate metabolism, and on genetic mutations in folate related genes associated with birth defects. Individual studies of the genetics of neural tube defects (NTDs) contain results on a small number of genes in each report. To identify genetic risk factors for NTDs, we evaluated potentially functional single nucleotide polymorphisms (SNPs) that are biologically plausible risk factors for NTDs but that have never been investigated for an association with NTDs, examined SNPs that previously showed no association with NTDs in published studies, and tried to confirm previously reported associations in folate-related and non-folate-related genes. We investigated 64 SNPs in 34 genes for association with spina bifida in up to 558 case families (520 cases, 507 mothers, 457 fathers) and 994 controls in Ireland. Case-control and mother-control comparisons of genotype frequencies, tests of transmission disequilibrium, and log-linear regression models were used to calculate effect estimates. Spina bifida was associated with over-transmission of the LEPR (leptin receptor) rs1805134 minor C allele genotype relative risk (GRR): 1.5;95% confidence interval (CI): 1.0-2.1;P = 0.0264 and the COMT (catechol-O-methyltransferase) rs737865 major T allele (GRR: 1.4;95% CI: 1.1-2.0;P = 0.0206). After correcting for multiple comparisons, these individual test P-values exceeded 0.05. Consistent with previous reports, spina bifida was associated with MTHFR 677C>T, T (Brachyury) rs3127334, LEPR K109R, and PDGFRA promoter haplotype combinations. The associations between LEPR SNPs and spina bifida suggest a possible mechanism for the finding that obesity is a NTD risk factor. The association between a variant in COMT and spina bifida implicates methylation and epigenetics in NTDs. Neural tube defects (NTDs) are common birth defects (1 in 1000 pregnancies in the US and Europe) that have complex origins, including environmental and genetic factors. A low level of maternal folate is one well-established risk factor, with maternal periconceptional folic acid supplementation reducing the occurrence of NTD pregnancies by 50-70%. Gene variants in the folate metabolic pathway (e.g., MTHFR rs1801133 (677 C >T) and MTHFD1 rs2236225 (R653Q)) have been found to increase NTD risk. We hypothesized that variants in additional folate/B12 pathway genes contribute to NTD risk. A tagSNP approach was used to screen common variation in 82 candidate genes selected from the folate/B12 pathway and NTD mouse models. We initially genotyped polymorphisms in 320 Irish triads (NTD cases and their parents), including 301 cases and 341 Irish controls to perform case-control and family based association tests. Significantly associated polymorphisms were genotyped in a secondary set of 250 families that included 229 cases and 658 controls. The combined results for 1441 SNPs were used in a joint analysis to test for case and maternal effects. Nearly 70 SNPs in 30 genes were found to be associated with NTDs at the p <0.01 level. The ten strongest association signals (p-value range: 0.0003-0.0023) were found in nine genes (MFTC, CDKN2A, ADA, PEMT, CUBN, GART, DNMT3A, MTHFD1 and T (Brachyury)) and included the known NTD risk factor MTHFD1 R653Q (rs2236225). The single strongest signal was observed in a new candidate, MFTC rs17803441 (OR = 1.61 1.23-2.08, p = 0.0003 for the minor allele). Though nominally significant, these associations did not remain significant after correction for multiple hypothesis testing. To our knowledge, with respect to sample size and scope of evaluation of candidate polymorphisms, this is the largest NTD genetic association study reported to date. The scale of the study and the stringency of correction are likely to have contributed to real associations failing to survive correction. We have produced a ranked list of variants with the strongest association signals. Variants in the highest rank of associations are likely to include true associations and should be high priority candidates for further study of NTD risk. Future investigations will explore genetic factors that have been shown to affect micronutrients of interest in our quantitative traits genome wide assocation study. For example, we have measured serum and red cell folate levels in over 2500 student volunteers and have generated genome wide data on their genetic variants. These data sets will be merged to determine the most important genetic factors that influence folate levels controlling for use of folic acid containing supplements and fortified food. These results will inform our investigation of genetic factors that are associated with neural tube defect risk. In addition we are collaborating with other groups to look for genetic variants that affect levels of other important chemicals. Von Willebrand factor has just been studied. The plasma glycoprotein von Willebrand factor (VWF) exhibits fivefold antigen level variation across the normal human population determined by both genetic and environmental factors. Low levels of VWF are associated with bleeding and elevated levels with increased risk for thrombosis, myocardial infarction, and stroke. To identify additional genetic determinants of VWF antigen levels and to minimize the impact of age and illness-related environmental factors, we performed genome-wide association analysis in two young and healthy cohorts (n = 1,152 and n = 2,310) and identified signals at ABO (P <7.9E-139) and VWF (P <5.5E-16), consistent with previous reports. Additionally, linkage analysis based on sibling structure within the cohorts, identified significant signals at chromosome 2q12-2p13 (LOD score 5.3) and at the ABO locus on chromosome 9q34 (LOD score 2.9) that explained 19.2% and 24.5% of the variance in VWF levels, respectively. Given its strong effect, the linkage region on chromosome 2 could harbor a potentially important determinant of bleeding and thrombosis risk. The absence of a chromosome 2 association signal in this or previous association studies suggests a causative gene harboring many genetic variants that are individually rare, but in aggregate common. These results raise the possibility that similar loci could explain a significant portion of the "missing heritability" for other complex genetic traits.

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VanderMeer, Julia E; Carter, Tonia C; Pangilinan, Faith et al. (2016) Evaluation of proton-coupled folate transporter (SLC46A1) polymorphisms as risk factors for neural tube defects and oral clefts. Am J Med Genet A 170A:1007-16
Szymczak, Silke; Holzinger, Emily; Dasgupta, Abhijit et al. (2016) r2VIM: A new variable selection method for random forests in genome-wide association studies. BioData Min 9:7
Ozel, A B; McGee, B; Siemieniak, D et al. (2016) Genome-wide studies of von Willebrand factor propeptide identify loci contributing to variation in propeptide levels and von Willebrand factor clearance. J Thromb Haemost 14:1888-98
Mills, James L; Dimopoulos, Aggeliki; Bailey, Regan L (2016) What is standing in the way of complete prevention of folate preventable neural tube defects? Birth Defects Res A Clin Mol Teratol 106:517-9
Deac, Oana M; Mills, James L; Shane, Barry et al. (2015) Tryptophan catabolism and vitamin B-6 status are affected by gender and lifestyle factors in healthy young adults. J Nutr 145:701-7
Wang, Yifan; Liu, Aiyi; Mills, James L et al. (2015) Pleiotropy analysis of quantitative traits at gene level by multivariate functional linear models. Genet Epidemiol 39:259-75
Carter, Tonia C; Pangilinan, Faith; Molloy, Anne M et al. (2015) Common Variants at Putative Regulatory Sites of the Tissue Nonspecific Alkaline Phosphatase Gene Influence Circulating Pyridoxal 5'-Phosphate Concentration in Healthy Adults. J Nutr 145:1386-93
Mills, James L (2015) Preventing folate-related neural tube defects: Problem solved, or not? Birth Defects Res A Clin Mol Teratol 103:469-70
Ozaki, Mari; Molloy, Anne M; Mills, James L et al. (2015) The Dihydrofolate Reductase 19 bp Polymorphism Is Not Associated with Biomarkers of Folate Status in Healthy Young Adults, Irrespective of Folic Acid Intake. J Nutr 145:2207-11
Bailey, Lynn B; Stover, Patrick J; McNulty, Helene et al. (2015) Biomarkers of Nutrition for Development-Folate Review. J Nutr 145:1636S-1680S

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